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I'd tell the Hasbro execs to go fuck themselves with a cactus, though probably not in those exact words. Different ways to be a girl was, as far as I know, a core idea of the show to start with. You are going to lose some of that point by turning some of the main characters to guys.
My instant response would be AJ and RD, because not much would change. Many have thought RD was a guy to begin with for some odd reason. Except then these two different, more non-stereotypical girl characters wouldn't be there anymore. You can be a nerd or an artist or a party girl or an animal lover, but not a farmer or an athlete. You could switch Rarity and Flutters to show that not all guys need to be tough guys or whatever, but then you lose those girl characters and end up giving a fairly one-sided representation of guys. You cannot pick and choose some of them to genderswap and still have the theme of "many ways to be a girl" as strong at all. And token guy characters might very well just bother people. I would think this is a situation where the only winning move is not to play, and even then you lose since there's no show.
Of course, it would be rather rude of me to just say I won't play, so…
How much of the show will be changed? Are the characters supposed to be exactly the same but just genderswapped? How will the whole Gala thing go? I cannot see it being a simple change and pretend nothing changed. Twilight's first sleepover and makeovers. What if one of them was a guy, would they still go along with it? Not that there'd be anything necessarily wrong with that, but it is a question.
All that said…
Assuming we don't go and change everything, this gives us two different mane guys. Rainbow Dash defending Flutterguy and being a closer friend with him is more preferable to me than having Dash be a guy who stood up for Fluttershy in flight camp, because strong guys standing up for "weaker" girls is such a boring old thing. Also he'd stand in stark contrast to Applejack, showing that there are more ways to be a guy, too. Applejack would balance that out, of course.
Applebloom I would go with simply to have one brother-brother, one sister-sister and one brother-sister relationship going on. Spike and Twi would be said brother-sister thing. You could argue for swapping Scootaloo and Spike but that's just not my preference.
This leaves us with Rarity, Twilight, Pinkie and Rainbow as the ladies of the cast, which while not really as varied as the M6 we have, would still have at least some variance and different types of girls one could be. The male selection isn't as good, but no can do.
Again, though, I'd much prefer not to do that. Instead I might give more screentime for Mac, bring in Shiny earlier and maybe have Pipsquek pop in earlier, as well. Telling someone you love a thing but that they should change the core idea of it isn't exactly the best thing to do, though, in my opinion. I can't help but think it would be a different show if that had happened from the start.